Awaken
by CSIBeauty
Summary: After returning from Manhattan, Hook suddenly falls off the radar. Emma goes looking for him and is surprised by what she finds. Hook is in trouble and Emma has to decide if she is willing to trust her feelings so she can save him. AU, Now Complete
1. Something's Not Right

_Chapter 1: Something's Not Right_

The week after Emma returned from Manhattan was nothing short of a nightmare. The last thing she had ever wanted to do was accept that Neal would be in her life again, but now she didn't really get much of a choice. Though she wanted nothing to do with him romantically, she couldn't deny Henry the chance to get to know his father. At this point Henry still wasn't really talking to her much. He was still mad about her lying to him about who his father really was. Then she had to deal with the fact that Neal was Gold's son. Another part of the growing family tree that she wished she could ignore.

Emma sighed staring down at the paperwork that was sitting in front of her. Work was becoming a welcome distraction, but right now she was finding it increasingly hard to focus. For some reason she kept feeling like something was wrong. She had no idea where the feeling was coming from. Despite her current stressful situation, everything in Storybrooke had been fairly quiet. Though she knew that Cora was still out there somewhere planning something, she had yet to make her move.

Maybe, it was just that she was worried about what Cora was planning. She did still feel like her family was in danger and she hated wondering what was going to happen next. Right now she would take any distraction she could get. She was hoping someone would steal something or get into a fight, just so she had something else to focus on right now. Hell, at this point she would take Hook and his shameless flirting and innuendos, but she hadn't seen him since he helped them get back to Storybrooke.

It was unusual for him. Usually she expected him to show up at every turn just to annoy her. He did seem to enjoy that, but lately he was nowhere to be found. In fact nobody had seen the pirate. Part of that worried her, though she wasn't sure why. Maybe he was plotting his revenge still. After all, he spent 300 years planning his revenge, it's not like the man wasn't patient. Still, she couldn't shake the bad feeling she had. Emma shook her head trying to get those thoughts out of her mind. The last thing she needed to be doing right now was worrying about Hook. There were far more pressing matters to attend to.

After staring at her paperwork for several more minutes, she realized that there was no way it was going to get done. She stood up from her desk and grabbed her coat. It was a little early, but she was supposed to be meeting Henry and Neal at Granny's for lunch. Though Emma really didn't want to spend any time with Neal at the moment, she agreed to for Henry's sake. It was the first time since they got back from Manhattan that he had actually invited her to do anything with him and she wanted to take the chance to let him know that she was sorry for lying to him.

Surprisingly, lunch went off without a hitch and it had put Emma in a much better mood. Henry seemed to enjoy the fact that she and Neal were able to get along together for a short amount of time and it appeared that Henry wasn't quite as angry at Emma anymore. That was a relief. She didn't like knowing Henry was mad at her, though he did seem to understand why she had lied, he still had been mad at her for it. Emma started to head back to the station when her mind began to wander back to Hook.

A week had passed without any sign of the pirate and Emma couldn't help, but wonder what that meant. He hadn't exactly decided to be very secretive as of late which made her worry that something had happened to him. Emma shook her head. It wasn't her job to be worried about the pirate. He was perfectly capable of taking care of himself a fact that he had made clear when they were in Manhattan. He wasn't so happy about her interfering with his revenge, but he had claimed that he didn't care if he died as long as Gold went with him. Emma had wondered how hard it was for him to go so many years wanting nothing more than to avenge the woman he loved, especially since he didn't care if he died to get his revenge. Emma decided it was best to just leave the pirate alone and get back to what she was supposed to be doing. Still when Emma returned to work she continued to have difficulty focusing on the task at hand.

After another hour or so of staring at the paperwork that just wasn't going to get done, Emma decided she should head out. There was no way she was going to be able to focus until she figured out what was going on with Hook. Whatever, it was she had a bad feeling about it. She decided the best place to look for the pirate would be on his ship. If he was planning anything he wouldn't likely spend too much time away from his little home. It was the only place in Storybrooke that the pirate spent most of his time. Most of the residents didn't care for the pirate for obvious reasons. Though he had no problem showing up at the station or her apartment to bug her, he didn't really go anywhere else.

As Emma approached the harbor where the invisible ship was docked, she couldn't help feeling like she wasn't going to like what she found. Something wasn't right, everything was quiet. Almost like nobody had been there in days. Though she expected to find Hook aboard his ship, she found that most of the seagulls were not hanging around like they used to. It was unnerving and Emma wasn't sure what that meant. It was almost like someone was trying to keep people away from the area. She drew her gun as she approached the invisible gangplank. She couldn't shake the bad feeling she had and she wasn't about to be unprepared if something were to happen.

When she had finally made it aboard the Jolly Roger the bad feeling she had got stronger. The sea was too calm. The ship wasn't swaying like it usually did. Almost like it's master wasn't home and maybe he wasn't. Maybe she had come all this way and worried for nothing. There was no way she was going to be able to focus until she made sure everything was okay with him. It appeared that the deck was abandoned so she headed to the only other place she could think that he would be. His captain's quarters.

Below deck was much darker than she anticipated. It made sense since it wasn't like he had electricity aboard his ship, but she had never actually been anywhere but the deck of the ship. Her eyes adjusted to the darkness after a few minutes and she headed down the hallway to where she assumed the captain's quarters would be. The large door was a good indication that she found what she was looking for. It had fancy writing on the door that just said, "The Captain," Emma smiled at the simplicity of it and wondered if it had always been like that or if Hook had done that himself when he became captain.

Without another thought Emma knocked on the wooden door and waited for someone to answer, but no answer came. She knocked again this time much harder, but there still was no answer. Emma put her ear up against the door to see if she could hear anything, but it was silent. Normally, she wouldn't find herself barging into the pirate's cabin when it was possible that he could be lurking around watching her, but she found that she didn't have any self-control in this moment. There was something wrong and she wasn't going to stand around and wait to see what would happen. When she opened the door to the cabin she was surprised to see Hook lying on his bed, sleeping. Was it possible that he just didn't hear her knocking?

"Hook?" Emma asked, as she approached the sleeping pirate. He didn't move. Fear began to well up inside her as she put her hand on his shoulder and shook. No response. "Hook?" she asked again, hoping to see the man open his eyes and throw out some flirty innuendo, but he remained silent.

That's when she realized that something was seriously wrong. He wasn't waking up and she had no idea why. She knew something wasn't right when he had stopped coming to harass her, but she was not prepared to find him like this. How long had he been like this and what was wrong with him? There was one last thing she could think of that might wake him up, but she doubted it would work.

"Killian?" Emma asked. She had never used his real name and she had hoped that it would prove that he was just messing with her. However, his eyes remained shut and his breathing stayed even. He wasn't going to wake up.


	2. Searching for Clues

_Chapter 2: Searching for Clues_

The sounds of the hospital were too familiar to her. They had been here not that long ago and she hoped that she wouldn't be back like this. The staff of the hospital were at a loss for what happened to Hook and Dr. Whale performed every test he could think of to find out why the pirate wouldn't wake up. Everything lead to a dead end. Emma wished she knew why she felt so scared for him. It's not like they were ever really friends, though they weren't exactly enemies either. For some reason she just wanted the man to open his eyes and give her one of the annoying smirks she had gotten so used to.

"Emma," She turned around to see Dr. Whale standing there with a clipboard in his hand.

"What's wrong with him?" she asked in a tone that was much harsher than she meant it to be.

"He's in a coma," Whale answered, simply.

"Why?" Emma asked when Whale didn't go into any more detail. "Why is he in a coma? People don't just slip into comas."

"I don't know why," Whale replied. "All of his blood work and tests came back negative. He's perfectly healthy."

"What about magic?" Emma asked. "It's not like this is any other normal town. Someone could have put him into a coma magically. Technically my father was in a coma magically before the curse was broken."

"Yes, and Mary Margaret read to him and he woke up," Whale remembered. "The problem is there is no way to detect what kind of magic it is. And in case you hadn't noticed, magic is not really my specialty. I'm more of a science type of guy."

"Well then you are really no use to me," Emma stated harshly.

"Look," Whale started. "We will keep him here and monitor him. You can go out and try to find out what type of magic this is and what needs to be done to wake him up. Just remember that if someone did this because they wanted him out of the way, they might not be too happy with you interfering in their plans."

"I'm perfectly capable of taking care of myself," said Emma, glancing back to the unconscious pirate in the hospital bed. She didn't like how weak and vulnerable he looked.

"I know you are," Whale replied. "But still be careful."

Emma just nodded without looking back at the doctor. She had a few ideas of who could have done this to Hook and some ideas of what kind of magic it was. However, she wasn't willing to jump to any conclusions without proof. The last thing she needed to do was to assume she knew what this was and end up being wrong. There was still so much about magic she didn't understand and she wondered how she was supposed to figure out what kind of magic this was with what little knowledge she had.

The first place she planned to look was the Jolly Roger. That was where she found Hook so it was where she was most likely to find any clues regarding what happened to him. David was on his way to the hospital after hearing what happened, but she really didn't want to stick around until he got there. Emma had no idea what kind of magic this was or if time was going to factor in waking the pirate. As she left the hospital she literally ran into someone walking by.

"Sorry," she said before looking up. "Neal?"

"Emma," he replied. "What are you doing at the hospital? Is everything okay?"

"Yes, and no," Emma replied. "I'm fine, Henry's fine."

"Then what's going on?" Neal asked.

"It's not your concern," she replied. "Now if you would excuse me, I'm kind of in the middle of something."

"If something is wrong, Emma, you can tell me," said Neal.

"You wouldn't care anyway," said Emma. However, Neal just stood there looking at her. She sighed. "Hook is in a coma okay."

"What?" Neal asked. "How?"

"I don't know," Emma replied. "I'm trying to figure that out."

"Why?" he replied.

"What?" Emma asked, confused.

"Why would you try to figure it out?" Neal explained. "You said he has been causing trouble since he came here. This way he is out of the way and you didn't have to do anything."

"I'm not just going to leave him like that," Emma replied. "I have no idea if whoever did that to him could come after someone else next. He may be a pain at times, but he has helped me before. Now I'm helping him."

"Why do you care?" Neal asked.

"I abandoned him on a beanstalk once," said Emma. Neal looked at her confused. "I did it because of you. Because of what you did to me I couldn't let myself trust him. I wanted to, but I was afraid so I chained him to the top of the beanstalk and left him there. I guess this is my way of telling him I'm sorry. I'm not just going to leave him like that. I'm going to find a way to wake him up."

"What if you can't?" said Neal.

"Then at least I tried," Emma replied, turning away and heading back toward the docks.

The last thing she needed was Neal interfering with what she was doing. She didn't want to admit to Neal that she did care about what happened to the pirate. Part of her panicked when she couldn't wake him up and she didn't really know why. At the very least she owed it to Hook to try to find a way to wake him up. It hurt when she realized that he wouldn't have left her like she had him and right now she wanted to make it up to him. At least that was the only reasonable excuse she could come up with for why she was willing to go through all the trouble to help the pirate.

Finally, she made it back to the pirate ship and rushed on board without a second thought. She figured that the best place to start looking for what happened would be where she found Hook. So she headed straight for the captains quarters. Several things in the cabin were strewn about on the floor from when the EMT's had got there. She wouldn't have been able to carry the unconscious pirate out herself. Other than the random items that had been knocked off of the nearby tables, the room seemed pretty well put together.

Emma began to gather the fallen items and sat them back on the tables and desk. She figured if she was going to figure out what happened it would be best to put the room back the way it was when she found it. Though it was difficult to do that when she hadn't really paid that much attention to where everything was when she entered. She was too focused on the unconscious pirate lying in bed. As she glanced around the room she couldn't find anything that seemed out of place. It looked as she would expect it to look, like a pirate's cabin.

There were pieces of gold strewn about each desk and table. There was a spyglass and several maps covering the table in the center of the room. Several bottles of rum were in the corner of the nearby desk, most of which were already empty. Nothing seemed like it didn't belong and Emma felt like she had hit a dead end. She sighed and sat down on the bed in the middle of the room putting her face in her hands. Tears began to fall and she attempted to fight them off. _Why the hell are you crying, Emma? _She thought to herself.

It didn't make any sense why she was so upset. She felt like she let him down and there was nothing she could do to help him. He wasn't going to wake up and for some reason she felt like that was her fault. She laid back in the bed, but felt something hard against her head and shot back up. At first glance there was nothing there, but when she pulled the top sheet back a small red vial was sitting on the bed. Emma gave it a curious glance before picking it up. That was definitely out of place. When she looked inside it had a few drops of some bluish liquid. It was obvious that whatever this was, is what put Hook into the coma.

However, Emma still had a very small amount of knowledge when it came to magic and she had no idea how to figure out what it was. There was one person in Storybrooke that would be able to find out what this was. She just really hoped she wouldn't have to ask Gold for help right now.


	3. Look Into the Mind

_Chapter 3: Look Into the Mind_

Despite Emma's better judgment she headed to Gold's shop. He was the only one who would be able to find out what the liquid in the red vial was, though she had no idea if he would actually agree to help her or not. If he knew that she was trying to find a way to help Hook he wouldn't be so happy to tell her what she wanted to know. The only good thing was that she had helped him far too many times in Manhattan and he would owe her for saving his life once they got back.

When Emma arrived at the shop Neal was already inside talking to his father. She wasn't sure if that would bode well for what she was coming for, but she had already made it this far and she wasn't about to give up now. The two men looked up at her when she entered and Emma wondered what the two men were talking about. However, that question was answered when Gold stood in front of Neal and gave her a smile that sent chills through her.

"I won't be helping you if you are helping that pirate," Gold stated.

Emma knew that was coming, but she wasn't going to back down without a fight. "I'm not asking you to help him," Emma stated. "I'm not asking you to cure him, or wake him. I just want to know what is in this vial."

Gold eyed the vial suspiciously. It was never easy to read the man so she had no idea if he could even tell her what was in it or if he even would.

"How about this, Miss Swan?" said Gold turning around and walking over to a nearby table. "I can't tell you what is in that vial. I can make assumptions, but I don't like to assume. However, if you can make this work, I'm sure you can figure out what was in that vial and what happened to your dear captain."

Gold turned around and held out a small dream catcher. The same one they used when they needed to see what Pongo had seen when they thought Archie had been killed.

"You expect me to use my magic?" Emma asked. "You started the magic when we went into Pongo's mind."

"Indeed, I did," said Gold, handing her the dream catcher. "However, I'm not going to be starting the magic this time. I said I'm not helping him. So you can figure out how to do that all on your own. If you can, then you have the answers you are looking for. If you can't, the captain won't be waking up anytime soon."

At this point, Emma didn't argue. It didn't usually get her anywhere with Gold and at least with this she had some kind of hope that she could make her magic work. She had never been able to will it to work for her much before, but she was desperate. Without another word she left the shop, refusing to look back at the two men standing there. She headed straight back to the hospital where both her father and mother were waiting, apparently for her.

"Emma?" Mary Margaret said, pulling her daughter into a hug. "Where have you been?"

"Trying to figure out what happened to, Hook," Emma replied, hugging her mother back. "All I have is a red vial and a dream catcher to work with."

"What?" Mary Margaret asked, confused.

"I found a red vial in Hook's bed," Emma explained holding it up. "And Gold gave me a dream catcher to try to look into his mind and figure out what happened."

"Do you know how to do that?" David asked.

"No," Emma admitted. "But I have to try."

Emma didn't wait for a reply before she walked into the pirate's room. He was right where she had left him and still looked as if he was sleeping peacefully. She had no idea how she was supposed to get the dream catcher to work; she didn't even know how she did it last time with the help from Gold. Still she wasn't going to give up. Mary Margaret and David stood several feet from Hook's bed watching as Emma attempted to use her magic.

Emma put all of her focus on the dream catcher as she let it trail over Hook's body, willing it to collect the memory of what happened before he went into the coma. She put the dream catcher in front of her and focused on making the memory appear in front of her. Nothing happened. She sighed and attempted to trail the dream catcher over the pirate's body again. This time it started to glow ever so lightly. She put the dream catcher in front of her again focusing all of her energy on getting the memory to appear. At first nothing happened, so she took a deep breath and tried again. This time the dream catcher began to glow bright and she could see the scene before her.

_Killian was looking down at a map of Storybrooke sitting on the table in the center of his cabin. Suddenly a voice spoke behind him._

"_Hello, Hook,"_

_He turned around to see Cora standing in front of him, an evil smile etched on her face._

"_Cora," he replied. "What are you doing here?"_

"_Well, I came to see you of course," she said. "Did you think we wouldn't find out that you lied about the location of the dagger?"_

"_So you're here to kill me then," Killian replied, no hint of fear in his voice._

"_Not quite," Cora stated. "That would be far too easy. I'm here to offer you a choice."_

"_I'm not interested in your games, Cora," said Killian._

"_Oh, this is no game," Cora replied. "I'm giving you an option." She pulled out the red vial she had tucked away in her jacket pocket. "And here it is. You are going to drink the potion in this vial."_

"_What makes you think I'm going to do that?" Killian asked. "Or are you planning to force it down my throat."_

"_I'm not forcing anything, dear," Cora stated. "This potion won't work if you don't take it willingly, but you will."_

"_And what makes you believe that?" he asked._

"_Because I'm giving you an option," Cora replied, with an evil smirk. "You either drink this potion or I will kill Emma Swan."_

_Killian swallowed hard. "What makes you think you can kill her? You already tried taking her heart and failed."_

"_There are other ways to kill people," said Cora with a smile. "I don't need to take her heart to do it. And I don't have to kill her. I'm giving you the option here. Drink the potion or I kill Emma. What is it going to be, Captain?"_

_Cora held the small red vial out to him. He grabbed it from her without hesitation and uncapped it. _

"_If I drink this," Killian started. "You won't harm her?"_

"_I won't," Cora replied._

"_Or her family," Killian added. "I'll drink this only if you promise that you will not hurt Emma or her family."_

"_Very well, Captain," Cora replied. "You drink that potion and I will stay away from Emma and her family."_

"_Can you at least tell me what this is going to do to me?" Killian asked, eyeing the vial._

"_Nothing too bad," Cora stated. "It will put you to sleep and you will stay asleep. The only way to wake you would be for your true love to kiss you. And I believe she is dead is she not?"_

"_Aye," Killian replied. "She is."_

"_Then there is no hope that you can be awakened," Cora stated. "Drink up, Captain."_

_Killian took a deep breath and drank the potion, before tossing the vial onto his bed. The last thing he saw before everything went black was Cora's evil smile. _


	4. Take a Chance

_Chapter 4: Take a Chance_

Emma dropped the dream catcher on the floor in shock, looking to the sleeping pirate in the bed next to her. He had done this to protect her. After everything they had been through she couldn't understand why he would care. She had chained him to a beanstalk, he locked her in a cage, she knocked him out with the compass, and yet he still drank the potion . . . to protect her. Emma felt a hand on her shoulder and looked to see Mary Margaret standing there with a sad smile.

"Why?" Emma asked. "Why would he drink a potion to protect me?"

"That's a question you would have to ask him," Mary Margaret replied. "I can guess, but I don't think you'd like what I'd have to say."

"What are you thinking?" Emma asked. "There is no way I can ask him. His true love is dead. There is no way we can wake him."

Mary Margaret looked back at David. "Maybe Milah wasn't his true love," she stated, looking back at Emma. "He gave up his life for you."

"What are you trying to say?" Emma asked. "That he loved me? That's not possible. He spent 300 years trying to avenge Milah's death."

"And then he gave that up for you," said Mary Margaret. "If he didn't care, then why didn't he just let Cora kill you? He could have had his revenge and you wouldn't be there to interfere. Emma, he gave up everything for you. I have a hard time believing that he doesn't have some feelings for you that weighed in on his decision."

"That's not possible," she repeated.

"Let me ask you this, Emma," said Mary Margaret. "Do you have feelings for him?"

"What?" Emma asked confused.

"Do you have feelings for him?" she repeated. "You have gone through a lot of trouble to try to help him. I know you probably want to believe that you would do this for anyone, but I think you are doing this because it's him."

"I. . ." Emma hesitated. "I don't have feelings for, Hook."

Her voice was weak and she wasn't sure she believed those words herself. This was much more than she was willing to deal with at the moment. There was no way that Captain Hook had any feelings for her. It just wasn't possible. Though she did have a hard time explaining why he would be willing to give up his own life to save hers and her families. That meant he had to care for her, but that didn't mean that he was in love with her.

"Emma?" Mary Margaret's voice pulled her out of her thoughts. "Maybe you should stay here and think."

"What's there to think about?" Emma asked. "I don't love, Hook and he doesn't love me. There is no way to save him."

"If there was even the slightest possibility that you are his true love," Mary Margaret started. "and kissing him could wake him, would you do it? Would you try?"

"I. . ." Emma started, unsure of her answer. She had been working so hard to find a way to bring him back, but she still couldn't believe that she would be his true love. "David you've been quiet through all of this."

"I'm not going to pretend I like Hook," said David. "But I can't deny what he did to protect you and our family. Even given his past, he gave up a lot to protect you and I can't help but respect that."

"So you're saying that you think he has feelings for me too," said Emma.

"I don't know," said David. "I can't pretend I know what the pirate is thinking, but he cares about you enough to give up his life. He went under that curse thinking he would never wake up and he was okay with that as long as you were safe. This is ultimately up to you. You have to decide what you want to do. If you kiss him and he doesn't wake up then nothing changes. What you're afraid of is what might change if he wakes."

"What makes you think I'm afraid?" Emma asked, barely able to contain the shakiness in her voice.

"I know that we haven't been in your life until recently, but we can tell that you've been hurt in the past," said Mary Margaret. "Someone you loved hurt you and you're afraid to try to love again. I told you once that those walls you build up can keep out pain, but it also keeps out love. Do you remember that?"

"Yes," Emma replied simply.

"Even before we knew who we were," Mary Margaret continued. "I could tell that someone caused you a lot of pain. Because of that you're afraid of what will happen if you let someone in, but sometimes when you let love in it can be amazing. It's a feeling that you will never get to know if you keep pushing people away and refusing to let anyone in. I'm not saying that I ever hoped that you would fall in love with Captain Hook or that he would be your true love, but I want you to have that opportunity. It doesn't matter who it is with as long as you are happy. True love is the most powerful magic of all, but you won't experience it if you don't take a chance on someone."

"You think I should take that chance on Hook?" Emma asked.

"You need to take a chance on someone," said Mary Margaret. "And he may be your true love. This is something you need to think about. We'll leave you alone, but remember that with the bad there is also good. I think that's true for him."

Emma just nodded as her parents left the room. This was never a position she ever thought she would find herself in. She never believed in true love until she found out who her parents were, and even then she was still skeptical. True love wasn't something she ever thought she was capable of having. Not after Neal. She didn't even think she believed in true love then, but it was the only time in her life that she was able to let someone in so easily. Hook had pretty much given up his life for her. How could she stand back and just ignore the possibility that she could wake him up?

However, Emma still wasn't sure she could deal with what that would mean. The possibility that Hook could be her true love was not something she was prepared for. She sat on the edge of his bed studying the man's face. He looked peaceful and not at all the dark pirate she was used to seeing. Part of her missed the smirks and flirty innuendos. She brushed the hair out of his face and smiled. Maybe her parents were right and she needed to stop being afraid of what might happen and take a chance.

Without another thought she brought her right hand up to his cheek and leaned in brushing her lips against his lightly. There was a surge of electricity that formed around her and she pulled back looking at his face for any sign that he was waking up. At first he was still, but then he took a deep breath and opened his eyes. Emma could feel the tears forming in her eyes as she smiled. He looked confused as his eyes adjusted to the light, and then they stopped on Emma. He smiled as he brought his right hand to rest on her cheek.

"I was hoping it'd be you," he stated.

Emma let out a strangled laugh and leaned in to kiss him again. He pulled her closer and she could feel the tears start to fall from her eyes. When she pulled back he wiped the tears away with his thumb.

"Don't cry, lass," he said.

"I thought I lost you," said Emma. "You gave up your life to protect me."

"I wouldn't be able to survive if someone killed the only other woman I've ever loved," he replied.

"You love me?" Emma asked, feeling the tears start to well up in her eyes again. He sat up straight in the bed, tucking a strand of hair behind her ear.

"More than you know, love," he answered, pulling her into another kiss. She sighed against his lips, moving both of her arms around his neck. He pulled away resting his forehead against hers.

"I think I might love you too," she stated with a smile.


End file.
